rs5756133

chr22-36297934-T-Achr22-36297934-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002473.6(MYH9):c.3101-920A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.464 in 152,024 control chromosomes in the GnomAD database, including 20,060 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.46 (20060 hom., cov: 32)
• Consequence: MYH9 NM_002473.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0960

Genes affected

MYH9 (HGNC:7579): (myosin heavy chain 9) This gene encodes a conventional non-muscle myosin; this protein should not be confused with the unconventional myosin-9a or 9b (MYO9A or MYO9B). The encoded protein is a myosin IIA heavy chain that contains an IQ domain and a myosin head-like domain which is involved in several important functions, including cytokinesis, cell motility and maintenance of cell shape. Defects in this gene have been associated with non-syndromic sensorineural deafness autosomal dominant type 17, Epstein syndrome, Alport syndrome with macrothrombocytopenia, Sebastian syndrome, Fechtner syndrome and macrothrombocytopenia with progressive sensorineural deafness. [provided by RefSeq, Dec 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.64 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYH9	NM_002473.6	c.3101-920A>T		intron_variant		ENST00000216181.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYH9	ENST00000216181.11	c.3101-920A>T		intron_variant		1	NM_002473.6	P1
MYH9	ENST00000685801.1	c.3164-920A>T		intron_variant
MYH9	ENST00000691109.1	n.3396-920A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.464 AC: 70532 AN: 151906 Hom.: 20061 Cov.: 32

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.784

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.458

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.483

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.464 AC: 70531 AN: 152024 Hom.: 20060 Cov.: 32 AF XY: 0.459 AC XY: 34111 AN XY: 74316

Gnomad4 AFR AF: 0.159

Gnomad4 AMR AF: 0.530

Gnomad4 ASJ AF: 0.485

Gnomad4 EAS AF: 0.137

Gnomad4 SAS AF: 0.311

Gnomad4 FIN AF: 0.596

Gnomad4 NFE AF: 0.645

Gnomad4 OTH AF: 0.478

Alfa AF: 0.538 Hom.: 2912

Bravo AF: 0.447

Asia WGS AF: 0.192 AC: 669 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.1
Dann	Benign	0.61

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs5756133; hg19: chr22-36693980;